[MMTK] a question about DNA and the Amber forcefield in MMTK

khinsen at cea.fr khinsen at cea.fr
Wed Sep 14 15:09:00 CEST 2005

On Sep 13, 2005, at 22:49, Kristina Woods wrote:

> ChemicalObjects.py", line 54, in __getattr__
>      return getattr(self.type, attr)
>  AttributeError: AtomType instance has no attribute 'amber_atom_type'
>  >>>
> ----------------------------------------------------------------------- 
> ---------------------------------------------------------
>  Could anyone possibly tell me what I am doing wrong or what I need to  
> define? 

To find out, I need to know which atom is concerned. Could you please  
re-run those few lines and after the crash type

	import pdb
	p self

Basically, there are two possibilities:
- The atom is part of a standard nucleic acid. Then something is  
missing in the MMTK database, and I would have to fix it.
- The atom is part of some molecule that is not in the MMTK database.  
You would then have to create a corresponding database entry and put  
the Amber parameters there.

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr

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